SeqTec

Getting Started

Getting Started

Data Formats

Data Formats
- FASTQ
- FASTA
- SAM / BAM / CRAM
- VCF / BCF
- BED
- GFF / GTF
- BigWig / bedGraph
- h5ad / AnnData
- MEX / 10x Format
- Hi-C Formats

Tools

Tools
- Quality Control
  - FastQC
  - fastp
  - MultiQC
  - NanoPlot
  - pycoQC
  - Chopper
- Alignment
  - BWA-MEM2
  - minimap2
  - Bowtie2
  - STAR
- SAM/BAM Processing
  - SAMtools
  - Sambamba
  - Picard
  - deepTools
- Interval Operations
  - BEDTools
- Genome Assembly
  - Flye
  - Canu
  - SPAdes
  - Unicycler
  - Medaka
- Assembly Quality Control
  - QUAST
  - BUSCO
- Genome Annotation
  - Bakta
  - Prokka
  - BRAKER
- Variant Calling
  - GATK
  - Clair3
  - FreeBayes
  - DeepVariant
- Variant Annotation
  - VEP (Variant Effect Predictor)
  - SnpEff
- Variant Processing
  - BCFtools
- Quantification
  - kallisto
  - Salmon
  - featureCounts
  - HTSeq
- Differential Expression
  - DESeq2
  - edgeR
- Single-Cell Analysis
  - Cell Ranger
  - STARsolo
  - Seurat
  - Scanpy
- Metagenomics
  - Kraken2
  - Bracken
  - Krona
- Epigenomics
  - MACS2
  - Bismark
- Basecalling
  - Dorado
  - Guppy
- Data Access
  - SRA Toolkit
  - Entrez Direct
- Visualization
  - IGV

Workflows

Workflows

Infrastructure

Infrastructure

Reference

Glossary

SeqTec

Infrastructure
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Infrastructure

Package managers, containers, and reproducible environments.

Conda / Mamba
Docker
Singularity / Apptainer

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